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worsica_ph1_resample_crop_rgb.py
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worsica_ph1_resample_crop_rgb.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# ========================================================================
# File: worsica_ph1_resample_crop_rgb.py
# This script is based on worsica-resampling.py created by Alberto Azevedo
#
# Main diferences between this one and the original are:
# 1- This script already applies Resampling and RGB, in one step.
# 2- This script already crops the imageset according to WKT the user provides
# (and this script automatically converts WKT to boundingbox)
# 3- This script uses a different file structure from the original
# (but later this needs to be refined)
# -----------------------------------------------------------------------
# Log:
# October 20, 2020: Applied some fixes from the worsica_resampling.py to here
# September 22, 2020: Initial version
# ========================================================================
__author__ = 'Ricardo Martins (original author: Alberto Azevedo)'
__doc__ = "Script to resample Sentinel 2 images to 10 m resolution"
__datetime__ = '& September 2020 &'
__email__ = 'rjmartins (original author: [email protected])'
# ========================================================================
import os
import gdal
import ogr
from pathlib import Path
from glob import glob
import numpy as np
import argparse
from multiprocessing import cpu_count
import shutil
import traceback
import zipfile
import worsica_common_script_functions
projWinArgs = None
def get_top_level_safe_dir(imgZip):
print('[get_top_level_safe_dir] Get .SAFE dir in ' + imgZip)
try:
folderNameSAFE = None
with zipfile.ZipFile(imgZip) as f:
finfolist = f.infolist()
if (len(finfolist) > 0):
for info in finfolist:
info_fn_split = info.filename.split('/')
if (len(info_fn_split) > 0):
if info_fn_split[0].endswith(".SAFE"):
print('[get_top_level_safe_dir] found ' + info_fn_split[0])
folderNameSAFE = info_fn_split[0]
print('[get_top_level_safe_dir] OK')
break
return folderNameSAFE
except Exception as e:
raise Exception('Error on getting SAFE name! Not found!!')
def get_top_level_tif_file(imgZip):
print('[get_top_level_tif_file] Get .TIF file in ' + imgZip)
try:
fileNameTIF = None
with zipfile.ZipFile(imgZip) as f:
finfolist = f.infolist()
if (len(finfolist) > 0):
for info in finfolist:
if '__MACOSX' not in info.filename: # do not search tif under __MACOSX
info_fn_split = info.filename.split('/')
if (len(info_fn_split) > 0):
if info_fn_split[-1].endswith(".tif"):
print('[get_top_level_tif_file] found ' + info_fn_split[-1])
fileNameTIF = info_fn_split[-1]
print('[get_top_level_tif_file] OK')
break
return fileNameTIF
except Exception as e:
raise Exception('Error on getting TIF filename! Not found!!')
def refitProjWin(ds1, projWin):
print('refitProjWin')
gt = ds1.GetGeoTransform()
maxH, maxW = ds1.RasterYSize, ds1.RasterXSize
ulx = gt[0]
uly = gt[3]
lrx = gt[0] + maxW * gt[1]
lry = gt[3] + maxH * gt[5]
print('raster')
print([ulx, uly, lrx, lry])
# check intersection
ring = ogr.Geometry(ogr.wkbLinearRing)
ring.AddPoint(ulx, uly)
ring.AddPoint(ulx, lry)
ring.AddPoint(lrx, uly)
ring.AddPoint(lrx, lry)
ring.AddPoint(ulx, uly)
rasterGeometry = ogr.Geometry(ogr.wkbPolygon)
rasterGeometry.AddGeometry(ring)
print('polygon')
print(projWin)
ulx2 = projWin[0]
uly2 = projWin[1]
lrx2 = projWin[2]
lry2 = projWin[3]
ring2 = ogr.Geometry(ogr.wkbLinearRing)
ring2.AddPoint(ulx2, uly2)
ring2.AddPoint(ulx2, lry2)
ring2.AddPoint(lrx2, uly2)
ring2.AddPoint(lrx2, lry2)
ring2.AddPoint(ulx2, uly2)
rasterGeometry2 = ogr.Geometry(ogr.wkbPolygon)
rasterGeometry2.AddGeometry(ring2)
if rasterGeometry2.Intersects(rasterGeometry):
print('Intersect!')
ulx2 = max(ulx, projWin[0])
uly2 = min(uly, projWin[1])
lrx2 = min(lrx, projWin[2])
lry2 = max(lry, projWin[3])
return ulx2, uly2, lrx2, lry2
else:
print('Does not insersect!')
return None, None, None, None
# -----------------
# RUN RESAMPLING AND RGB
# -----------------
def worsicaResamplingRGB(procDicts):
worsicaResampling(procDicts, 'rgb')
def worsicaRGB(imgZip, procDict, fileLista, actual_path):
print('worsicaRGB')
try:
BandsRGB = {}
if 'uploaded-user' in imgZip: # if its an uploaded file
# if has set bands: 'redband=1;greenband=2;blueband=3;nirband=4'
if 'bands' in procDict and procDict['bands'] != "auto":
bands = procDict['bands'].replace('band', '') # 'red=1;green=2;blue=3;nir=4'
bands = bands.replace(
'red',
'R').replace(
'green',
'G').replace(
'blue',
'B').replace(
'nir',
'NIR') # 'R=1;G=2;B=3;NIR=4'
bandsList = bands.split(';') # ['R=1', 'G=2', 'B=3', 'NIR=4']
tifFile = get_top_level_tif_file(imgZip)
ds3 = gdal.Open(actual_path + "/resampled/" + tifFile[:-4] + "_resampled.tif")
for bL in bandsList:
b = bL.split('=')
ds3b = ds3.GetRasterBand(int(b[1]))
BandsRGB[b[0]] = ds3b.GetDataset()
print('Loaded ' + b[0] + ' as band ' + str(b[1]))
fout2 = actual_path + "/resampled/" + tifFile[:-4] + "_RGB.tif"
print(fout2)
projWinArgs = procDict['projWinArgs']
ulx2, uly2, lrx2, lry2 = refitProjWin(ds3, projWinArgs['projWin'])
outputBounds = (min(ulx2, lrx2), min(uly2, lry2), max(ulx2, lrx2), max(uly2, lry2))
print(outputBounds)
vrt_options = gdal.BuildVRTOptions(
outputBounds=outputBounds, separate=True, hideNodata=True)
gdal.BuildVRT(actual_path + '/auxRGB/auxRGB.vrt',
[BandsRGB['R'], BandsRGB['G'], BandsRGB['B']], options=vrt_options)
ds2 = gdal.Open(actual_path + '/auxRGB/auxRGB.vrt')
NUM_THREADS = str(cpu_count())
print('NUM_THREADS=' + NUM_THREADS)
ds2 = gdal.Translate(
fout2,
ds2,
creationOptions=[
"NUM_THREADS=" +
NUM_THREADS,
"COMPRESS=LZW",
"PREDICTOR=2",
"TILED=YES"])
ds2 = None
else:
raise Exception('Error: No bands list set for an uploaded file!')
else:
if 'L2A' in imgZip:
l10JP2 = [
i for i in fileLista if (
i.endswith("B02_10m.jp2") or i.endswith("B03_10m.jp2") or i.endswith("B04_10m.jp2"))]
elif 'L1C' in imgZip:
l10JP2 = [
i for i in fileLista if (
i.endswith("B02.jp2") or i.endswith("B03.jp2") or i.endswith("B04.jp2"))]
l1020 = l10JP2
pathAux = Path(actual_path) / 'auxResample'
pathAux.mkdir(exist_ok=True)
for img in l1020:
fout = "".join((str(pathAux), "/", img.split("SAFE")
[0][:-1], img.split("/")[-1][-12:-4], ".tif"))
fout2 = actual_path + "/" + "_".join((img.split("SAFE")[0][:-1], "RGB.tif"))
if "B02" in fout: # "B02_10m"
BandsRGB["B"] = fout
elif "B03" in fout: # "B03_10m"
BandsRGB["G"] = fout
elif "B04" in fout: # "B04_10m"
BandsRGB["R"] = fout
vrt_options = gdal.BuildVRTOptions(separate=True, hideNodata=True)
gdal.BuildVRT(actual_path + '/auxRGB/auxRGB.vrt',
[BandsRGB['R'], BandsRGB['G'], BandsRGB['B']], options=vrt_options)
ds2 = gdal.Open(actual_path + '/auxRGB/auxRGB.vrt')
ds2 = gdal.Translate(fout2, ds2, outputType=gdal.GDT_Float32)
ds2 = None
print(f"{fout2} :: Done!!!")
# return None
except Exception as e:
print(traceback.format_exc())
exit(1)
# -----------------
# RUN ONLY RESAMPLING
# -----------------
def worsicaResampling(procDicts, mode='normal'):
for procDict in procDicts:
try:
imgZip = procDict['imgZip']
projWinArgs = procDict['projWinArgs']
if ('path' in procDict):
ACTUAL_PATH = procDict['path']
else:
ACTUAL_PATH = os.getcwd()
print(ACTUAL_PATH)
BandsRGB = {}
print(procDict['bands'])
if 'uploaded-user' in imgZip: # if its an uploaded file
# if has set bands: 'redband=1;greenband=2;blueband=3;nirband=4'
if 'bands' in procDict and procDict['bands'] != "auto":
foutFiles = []
unzipcmd = worsica_common_script_functions._run_unzip(imgZip, ACTUAL_PATH)
if unzipcmd != 0:
print('Error on unzip! Corrupt file!!')
raise Exception('Error on unzip! Corrupt file!!')
bands = procDict['bands'].replace('band', '') # 'red=1;green=2;blue=3;nir=4'
bands = bands.replace(
'red',
'R').replace(
'green',
'G').replace(
'blue',
'B').replace(
'nir',
'NIR') # 'R=1;G=2;B=3;NIR=4'
bandsList = bands.split(';') # ['R=1', 'G=2', 'B=3', 'NIR=4']
tifFile = get_top_level_tif_file(imgZip)
fileLista = [ACTUAL_PATH + '/' + tifFile]
foutFiles.append(ACTUAL_PATH + '/' + tifFile)
ds3 = gdal.Open(ACTUAL_PATH + '/' + tifFile)
# This step is REQUIRED in order to provide the correct output on the visualization.
# The wrap is used to convert the imageset from any EPSG to EPSG:4326
print('gdal.warp')
fout_wrap = ACTUAL_PATH + "/auxResample/" + "_".join((tifFile[:-4], "wrap.tif"))
print(fout_wrap)
foutFiles.append(fout_wrap)
ds1 = gdal.Warp(
fout_wrap,
ds3,
srcNodata=-32767,
dstNodata=0,
dstSRS=projWinArgs['projWinSRS'],
format='GTiff',
multithread=True,
outputType=gdal.GDT_Float32)
ds3 = None
# refit projwin according to the raster extent
ulx2, uly2, lrx2, lry2 = refitProjWin(ds1, projWinArgs['projWin'])
projWin = [ulx2, uly2, lrx2, lry2]
print(projWin)
NUM_THREADS = str(cpu_count())
print('NUM_THREADS=' + NUM_THREADS)
ds3 = gdal.Open(fout_wrap, gdal.GA_Update)
ds1 = None
BandsRGBTranslate = {}
for bL in bandsList:
b = bL.split('=')
ds3b = ds3.GetRasterBand(int(b[1]))
BandsRGB[b[0]] = ds3b.GetDataset()
BandsRGBTranslate[b[0]] = int(b[1])
print('Loaded ' + b[0] + ' as band ' + str(b[1]))
BandsLTranslate = [
BandsRGBTranslate['B'],
BandsRGBTranslate['G'],
BandsRGBTranslate['R'],
BandsRGBTranslate['NIR']]
# no SWIR1 and SWIR2
fout2 = ACTUAL_PATH + "/resampled/" + "_".join((tifFile[:-4], "resampled.tif"))
print(fout2)
Metadata = ds3.GetMetadata()
Description = ds3.GetDescription()
print('gdal.buildVRT')
outputBounds = (min(ulx2, lrx2), min(uly2, lry2),
max(ulx2, lrx2), max(uly2, lry2))
print(outputBounds)
vrt_options = gdal.BuildVRTOptions(
outputBounds=outputBounds, separate=False, hideNodata=True)
gdal.BuildVRT(ACTUAL_PATH + '/auxResample/aux.vrt',
[BandsRGB['B'],
BandsRGB['G'],
BandsRGB['R'],
BandsRGB['NIR']],
options=vrt_options)
ds2 = gdal.Open(ACTUAL_PATH + '/auxResample/aux.vrt')
print(BandsLTranslate)
ds2 = gdal.Translate(
fout2,
ds2,
bandList=BandsLTranslate,
creationOptions=[
"NUM_THREADS=" +
NUM_THREADS,
"COMPRESS=LZW",
"PREDICTOR=2",
"TILED=YES"])
ds2 = None
print('Update statistics...')
ds3 = gdal.Open(fout2, gdal.GA_Update)
for bL in bandsList:
b = bL.split('=')
band = ds3.GetRasterBand(int(b[1]))
band.ComputeStatistics(0)
band.FlushCache()
band = None
print('Updated stats for band ' + str(b[1]))
ds3.FlushCache()
ds3 = None
else:
raise Exception('Error: No bands list set for an uploaded file!')
else:
unzipcmd = worsica_common_script_functions._run_unzip(imgZip)
print(unzipcmd)
if unzipcmd != 0:
print('Error on unzip! Corrupt file!!')
raise Exception('Error on unzip! Corrupt file!!')
fileLista = []
getSAFEFolderName = get_top_level_safe_dir(imgZip) # f"{imgZip[:-4]}.SAFE"
for root, dirs, files in os.walk(getSAFEFolderName, topdown=True):
for name in files:
fileLista.append(os.path.join(root, name))
for name in dirs:
fileLista.append(os.path.join(root, name))
if 'L2A' in imgZip:
l10JP2 = [i for i in fileLista if (i.endswith("B02_10m.jp2") or i.endswith(
"B03_10m.jp2") or i.endswith("B04_10m.jp2") or i.endswith("B08_10m.jp2"))]
l20JP2 = [i for i in fileLista if i.endswith(
"B11_20m.jp2") or i.endswith("B12_20m.jp2")]
elif 'L1C' in imgZip:
l10JP2 = [i for i in fileLista if (i.endswith("B02.jp2") or i.endswith(
"B03.jp2") or i.endswith("B04.jp2") or i.endswith("B08.jp2"))]
l20JP2 = [
i for i in fileLista if (
i.endswith("B11.jp2") or i.endswith("B12.jp2"))]
l1020 = l10JP2 + l20JP2
foutFiles = []
for img in l1020:
fout = "".join((ACTUAL_PATH + "/auxResample/", img.split("SAFE")
[0][:-1], img.split("/")[-1][-12:-4], ".tif"))
fout2 = ACTUAL_PATH + "/resampled/" + \
"_".join((img.split("SAFE")[0][:-1], "resampled.tif"))
foutFiles.append(fout)
fout_wrap = "".join((ACTUAL_PATH + "/auxResample/", img.split("SAFE")
[0][:-1], img.split("/")[-1][-12:-4], "_wrap.tif"))
foutFiles.append(fout_wrap)
ds = gdal.Open(img, gdal.GA_Update)
band = ds.GetRasterBand(1)
arr = band.ReadAsArray()
[cols, rows] = arr.shape
Metadata = ds.GetMetadata()
GCPs = ds.GetGCPs()
GCPsProj = ds.GetGCPProjection()
geotransform = ds.GetGeoTransform()
Description = ds.GetDescription()
#
arr2 = np.where(arr < 0, 0, arr)
band.WriteArray(arr2)
band.SetNoDataValue(0)
ds.FlushCache()
# This step is REQUIRED in order to provide the correct output on the visualization.
# The wrap is used to convert the imageset from any EPSG to EPSG:4326
print('gdal.warp')
ds1 = gdal.Warp(
fout_wrap,
ds,
dstSRS=projWinArgs['projWinSRS'],
format='GTiff',
multithread=True,
outputType=gdal.GDT_Float32)
# The translate is required to crop the imageset according to the ROI
print('gdal.translate')
gdal.Translate(
fout,
ds1,
format="GTiff",
resampleAlg='cubic',
outputType=gdal.GDT_Float32,
projWinSRS=projWinArgs['projWinSRS'],
projWin=projWinArgs['projWin'])
ds = None
ds1 = None
if "B02" in fout: # "B02_10m"
BandsRGB["B"] = fout
print(str(fout))
elif "B03" in fout: # "B03_10m"
BandsRGB["G"] = fout
print(str(fout))
elif "B04" in fout: # "B04_10m"
BandsRGB["R"] = fout
print(str(fout))
elif "B08" in fout: # "B08_10m"
BandsRGB["NIR"] = fout
print(str(fout))
elif "B11" in fout: # "B11_20m"
BandsRGB["SWIR1"] = fout
print(str(fout))
elif "B12" in fout: # "B12_20m"
BandsRGB["SWIR2"] = fout
print(str(fout))
print(BandsRGB)
vrt_options = gdal.BuildVRTOptions(separate=True, hideNodata=True)
gdal.BuildVRT(ACTUAL_PATH + '/auxResample/aux.vrt',
[BandsRGB['B'],
BandsRGB['G'],
BandsRGB['R'],
BandsRGB['NIR'],
BandsRGB['SWIR1'],
BandsRGB['SWIR2']],
options=vrt_options)
ds2 = gdal.Open(ACTUAL_PATH + '/auxResample/aux.vrt')
ds2 = gdal.Translate(fout2, ds2)
ds2 = None
dsOut = gdal.Open(fout2)
dsOut.SetMetadata(Metadata)
dsOut.SetDescription(Description)
dsOut.GetRasterBand(1).SetDescription('Blue')
dsOut.GetRasterBand(2).SetDescription('Green')
dsOut.GetRasterBand(3).SetDescription('Red')
dsOut.GetRasterBand(4).SetDescription('NIR')
if 'uploaded-user' in imgZip: # if its an uploaded file
print('Skip: No description for swir1 and swir2')
else:
dsOut.GetRasterBand(5).SetDescription('SWIR1')
dsOut.GetRasterBand(6).SetDescription('SWIR2')
dsOut = None
if mode == 'rgb':
worsicaRGB(imgZip, procDict, fileLista, ACTUAL_PATH)
foutFiles.append(ACTUAL_PATH + "/auxResample/aux.vrt")
for trash in foutFiles:
os.remove(trash)
if 'uploaded-user' in imgZip:
pass
else:
fDelete = getSAFEFolderName
shutil.rmtree(f"{fDelete}")
print(f"{fout2} :: Done!!!")
return None
except Exception as e:
print(traceback.format_exc())
exit(1)
# -----------------
# RUN ONLY RESAMPLING WATER LEAK
# DIFFERENCE: Apply cloud removal to the resample
# WARNING: DO NOT USE IT FOR L1C
# -----------------
def worsicaResamplingWaterLeakRGB(procDicts):
for procDict in procDicts:
try:
imgZip = procDict['imgZip']
projWinArgs = procDict['projWinArgs']
if ('path' in procDict):
ACTUAL_PATH = procDict['path']
else:
ACTUAL_PATH = os.getcwd()
unzipcmd = worsica_common_script_functions._run_unzip(imgZip)
if unzipcmd != 0:
print('Error on unzip! Corrupt file!!')
raise Exception('Error on unzip! Corrupt file!!')
fileLista = []
getSAFEFolderName = get_top_level_safe_dir(imgZip) # f"{imgZip[:-4]}.SAFE"
for root, dirs, files in os.walk(getSAFEFolderName, topdown=True):
for name in files:
fileLista.append(os.path.join(root, name))
for name in dirs:
fileLista.append(os.path.join(root, name))
if 'L2A' in imgZip:
l10JP2 = [i for i in fileLista if (i.endswith("B02_10m.jp2") or i.endswith(
"B03_10m.jp2") or i.endswith("B04_10m.jp2") or i.endswith("B08_10m.jp2"))]
l20JP2 = [
i for i in fileLista if (
i.endswith("B11_20m.jp2") or i.endswith("B12_20m.jp2") or i.endswith("SCL_20m.jp2"))]
elif 'L1C' in imgZip:
l10JP2 = [i for i in fileLista if (i.endswith("B02.jp2") or i.endswith(
"B03.jp2") or i.endswith("B04.jp2") or i.endswith("B08.jp2"))]
l20JP2 = [i for i in fileLista if (i.endswith("B11.jp2") or i.endswith("B12.jp2"))]
l1020 = l10JP2 + l20JP2
BandsRGB = {}
foutFiles = []
print('--Start resampling the images (wrap and translate)')
for img in l1020:
fout = "".join((ACTUAL_PATH + "/auxResample/", img.split("SAFE")
[0][:-1], img.split("/")[-1][-12:-4], ".tif"))
fout2 = ACTUAL_PATH + "/resampled/" + \
"_".join((img.split("SAFE")[0][:-1], "resampled.tif"))
foutFiles.append(fout)
fout_wrap = "".join((ACTUAL_PATH + "/auxResample/", img.split("SAFE")
[0][:-1], img.split("/")[-1][-12:-4], "_wrap.tif"))
foutFiles.append(fout_wrap)
ds = gdal.Open(img, gdal.GA_Update)
band = ds.GetRasterBand(1)
arr = band.ReadAsArray()
[cols, rows] = arr.shape
Metadata = ds.GetMetadata()
GCPs = ds.GetGCPs()
GCPsProj = ds.GetGCPProjection()
geotransform = ds.GetGeoTransform()
Description = ds.GetDescription()
#
arr2 = np.where(arr < 0, 0, arr)
band.WriteArray(arr2)
band.SetNoDataValue(0)
ds.FlushCache()
# This step is REQUIRED in order to provide the correct output on the visualization.
# The wrap is used to convert the imageset from any EPSG to EPSG:4326 (projWinSRS)
print('gdal.wrap ')
ds1 = gdal.Warp(
fout_wrap,
ds,
dstSRS=projWinArgs['projWinSRS'],
format='GTiff',
multithread=True,
outputType=gdal.GDT_Float32)
# The translate is required to crop the imageset according to the ROI
print('gdal.translate ')
gdal.Translate(
fout,
ds1,
format="GTiff",
resampleAlg='cubic',
outputType=gdal.GDT_Float32,
projWinSRS=projWinArgs['projWinSRS'],
projWin=projWinArgs['projWin'])
ds = None
ds1 = None
if "B02" in fout: # "B02_10m"
BandsRGB["B"] = fout
elif "B03" in fout: # "B03_10m"
BandsRGB["G"] = fout
elif "B04" in fout: # "B04_10m"
BandsRGB["R"] = fout
elif "B08" in fout: # "B08_10m"
BandsRGB["NIR"] = fout
elif "B11" in fout: # "B11_20m"
BandsRGB["SWIR1"] = fout
elif "B12" in fout: # "B12_20m"
BandsRGB["SWIR2"] = fout
elif "SCL" in fout: # "SCL_20m"
BandsRGB["SCL"] = fout
print('--Convert vrt to tif')
# hideNodata=False, srcNodata="0 0 0 0 0 0")
vrt_options = gdal.BuildVRTOptions(separate=True, hideNodata=True)
if 'L2A' in imgZip:
gdal.BuildVRT(ACTUAL_PATH + '/auxResample/aux.vrt',
[BandsRGB['B'],
BandsRGB['G'],
BandsRGB['R'],
BandsRGB['NIR'],
BandsRGB['SWIR1'],
BandsRGB['SWIR2'],
BandsRGB["SCL"]],
options=vrt_options)
else:
gdal.BuildVRT(ACTUAL_PATH + '/auxResample/aux.vrt',
[BandsRGB['B'],
BandsRGB['G'],
BandsRGB['R'],
BandsRGB['NIR'],
BandsRGB['SWIR1'],
BandsRGB['SWIR2']],
options=vrt_options)
ds2 = gdal.Open(ACTUAL_PATH + '/auxResample/aux.vrt')
ds2 = gdal.Translate(fout2, ds2)
ds2 = None
print('--Insert metadata')
dsOut = gdal.Open(fout2)
dsOut.SetMetadata(Metadata)
dsOut.SetDescription(Description)
dsOut.GetRasterBand(1).SetDescription('Blue')
dsOut.GetRasterBand(2).SetDescription('Green')
dsOut.GetRasterBand(3).SetDescription('Red')
dsOut.GetRasterBand(4).SetDescription('NIR')
dsOut.GetRasterBand(5).SetDescription('SWIR1')
dsOut.GetRasterBand(6).SetDescription('SWIR2')
if 'L2A' in imgZip:
dsOut.GetRasterBand(7).SetDescription('SCL')
dsOut = None
# start cloud filtering
if 'L2A' in imgZip:
print('--Start cloud filtering')
dsOut = gdal.Open(fout2, gdal.GA_Update)
arrCloudMask = np.array(dsOut.GetRasterBand(7).ReadAsArray()).astype(int)
for i in range(1, 7):
b = dsOut.GetRasterBand(i)
# 0: NODATA, 8: CLOUD_MEDIUM_PROB, 9: CLOUD_HIGH_PROB, 10: THIN_CIRRUS
filterClasses = [0, 8, 9, 10]
for f in filterClasses:
b.WriteArray(np.where((arrCloudMask == f), 0, b.ReadAsArray()))
b.SetNoDataValue(0)
dsOut.FlushCache()
dsOut = None
worsicaRGB(imgZip, procDict, fileLista, ACTUAL_PATH)
print('--Remove files')
foutFiles.append(ACTUAL_PATH + "/auxResample/aux.vrt")
for trash in foutFiles:
os.remove(trash)
fDelete = getSAFEFolderName # imgZip.replace(".zip", ".SAFE")
shutil.rmtree(f"{fDelete}")
print(f"{fout2} :: Done!!!")
return None
except Exception as e:
print(traceback.format_exc())
exit(1)
def worsicaResamplingWaterLeak(procDicts):
for procDict in procDicts:
try:
imgZip = procDict['imgZip']
projWinArgs = procDict['projWinArgs']
if ('path' in procDict):
ACTUAL_PATH = procDict['path']
else:
ACTUAL_PATH = os.getcwd()
unzipcmd = worsica_common_script_functions._run_unzip(imgZip)
if unzipcmd != 0:
print('Error on unzip! Corrupt file!!')
raise Exception('Error on unzip! Corrupt file!!')
fileLista = []
getSAFEFolderName = get_top_level_safe_dir(imgZip)
for root, dirs, files in os.walk(getSAFEFolderName, topdown=True):
for name in files:
fileLista.append(os.path.join(root, name))
for name in dirs:
fileLista.append(os.path.join(root, name))
if 'L2A' in imgZip:
l10JP2 = [i for i in fileLista if (i.endswith("B02_10m.jp2") or i.endswith(
"B03_10m.jp2") or i.endswith("B04_10m.jp2") or i.endswith("B08_10m.jp2"))]
l20JP2 = [
i for i in fileLista if (
i.endswith("B11_20m.jp2") or i.endswith("B12_20m.jp2") or i.endswith("SCL_20m.jp2"))]
elif 'L1C' in imgZip:
l10JP2 = [i for i in fileLista if (i.endswith("B02.jp2") or i.endswith(
"B03.jp2") or i.endswith("B04.jp2") or i.endswith("B08.jp2"))]
l20JP2 = [i for i in fileLista if (i.endswith("B11.jp2") or i.endswith("B12.jp2"))]
l1020 = l10JP2 + l20JP2
BandsRGB = {}
foutFiles = []
print('--Start resampling the images (wrap and translate)')
for img in l1020:
fout = "".join((ACTUAL_PATH + "/auxResample/", img.split("SAFE")
[0][:-1], img.split("/")[-1][-12:-4], ".tif"))
fout2 = ACTUAL_PATH + "/resampled/" + \
"_".join((img.split("SAFE")[0][:-1], "resampled.tif"))
foutFiles.append(fout)
fout_wrap = "".join((ACTUAL_PATH + "/auxResample/", img.split("SAFE")
[0][:-1], img.split("/")[-1][-12:-4], "_wrap.tif"))
foutFiles.append(fout_wrap)
ds = gdal.Open(img, gdal.GA_Update)
band = ds.GetRasterBand(1)
arr = band.ReadAsArray()
[cols, rows] = arr.shape
Metadata = ds.GetMetadata()
GCPs = ds.GetGCPs()
GCPsProj = ds.GetGCPProjection()
geotransform = ds.GetGeoTransform()
Description = ds.GetDescription()
#
arr2 = np.where(arr < 0, 0, arr)
band.WriteArray(arr2)
band.SetNoDataValue(0)
ds.FlushCache()
# This step is REQUIRED in order to provide the correct output on the visualization.
# The wrap is used to convert the imageset from any EPSG to EPSG:4326 (projWinSRS)
print(str(img))
print('gdal.wrap ')
ds1 = gdal.Warp(
fout_wrap,
ds,
dstSRS=projWinArgs['projWinSRS'],
format='GTiff',
multithread=True,
outputType=gdal.GDT_Float32)
# The translate is required to crop the imageset according to the ROI
print('gdal.translate ')
gdal.Translate(
fout,
ds1,
format="GTiff",
resampleAlg='cubic',
outputType=gdal.GDT_Float32,
projWinSRS=projWinArgs['projWinSRS'],
projWin=projWinArgs['projWin'])
ds = None
ds1 = None
if "B02" in fout: # "B02_10m"
BandsRGB["B"] = fout
elif "B03" in fout: # "B03_10m"
BandsRGB["G"] = fout
elif "B04" in fout: # "B04_10m"
BandsRGB["R"] = fout
elif "B08" in fout: # "B08_10m"
BandsRGB["NIR"] = fout
elif "B11" in fout: # "B11_20m"
BandsRGB["SWIR1"] = fout
elif "B12" in fout: # "B12_20m"
BandsRGB["SWIR2"] = fout
elif "SCL" in fout: # "SCL_20m"
BandsRGB["SCL"] = fout
print('--Convert vrt to tif')
# hideNodata=False, srcNodata="0 0 0 0 0 0")
vrt_options = gdal.BuildVRTOptions(separate=True, hideNodata=True)
if 'L2A' in imgZip:
gdal.BuildVRT(ACTUAL_PATH + '/auxResample/aux.vrt',
[BandsRGB['B'],
BandsRGB['G'],
BandsRGB['R'],
BandsRGB['NIR'],
BandsRGB['SWIR1'],
BandsRGB['SWIR2'],
BandsRGB["SCL"]],
options=vrt_options)
else:
gdal.BuildVRT(ACTUAL_PATH + '/auxResample/aux.vrt',
[BandsRGB['B'],
BandsRGB['G'],
BandsRGB['R'],
BandsRGB['NIR'],
BandsRGB['SWIR1'],
BandsRGB['SWIR2']],
options=vrt_options)
ds2 = gdal.Open(ACTUAL_PATH + '/auxResample/aux.vrt')
ds2 = gdal.Translate(fout2, ds2)
ds2 = None
print('--Insert metadata')
dsOut = gdal.Open(fout2)
dsOut.SetMetadata(Metadata)
dsOut.SetDescription(Description)
dsOut.GetRasterBand(1).SetDescription('Blue')
dsOut.GetRasterBand(2).SetDescription('Green')
dsOut.GetRasterBand(3).SetDescription('Red')
dsOut.GetRasterBand(4).SetDescription('NIR')
dsOut.GetRasterBand(5).SetDescription('SWIR1')
dsOut.GetRasterBand(6).SetDescription('SWIR2')
if 'L2A' in imgZip:
dsOut.GetRasterBand(7).SetDescription('SCL')
dsOut = None
# start cloud filtering
if 'L2A' in imgZip:
print('--Start cloud filtering')
dsOut = gdal.Open(fout2, gdal.GA_Update)
arrCloudMask = np.array(dsOut.GetRasterBand(7).ReadAsArray()).astype(int)
for i in range(1, 7):
b = dsOut.GetRasterBand(i)
# 0: NODATA, 8: CLOUD_MEDIUM_PROB, 9: CLOUD_HIGH_PROB, 10: THIN_CIRRUS
filterClasses = [0, 8, 9, 10]
for f in filterClasses:
b.WriteArray(np.where((arrCloudMask == f), -999, b.ReadAsArray()))
b.SetNoDataValue(-999)
b.FlushCache()
b = None
dsOut.FlushCache()
dsOut = None
print('--Remove files')
foutFiles.append(ACTUAL_PATH + "/auxResample/aux.vrt")
for trash in foutFiles:
os.remove(trash)
fDelete = getSAFEFolderName
shutil.rmtree(f"{fDelete}")
print(f"{fout2} :: Done!!!")
return None
except Exception as e:
print(traceback.format_exc())
exit(1)
# ---------------
# RUN ONLY RGB FROM RESAMPLING TIF
# ---------------
def run_rgb(tifFile, ACTUAL_PATH, bandList=[3, 2, 1]):
try:
ds = gdal.Open(tifFile)
filename = tifFile.split('/')[-1][:-4]
fout2 = ACTUAL_PATH + "/" + filename + "_RGB.tif"
NUM_THREADS = str(cpu_count())
print('NUM_THREADS=' + NUM_THREADS)
gdal.Translate(
fout2,
ds,
format="GTiff",
bandList=bandList,
outputType=gdal.GDT_Float32,
creationOptions=[
"NUM_THREADS=" +
NUM_THREADS,
"COMPRESS=LZW",
"PREDICTOR=2",
"TILED=YES"])
ds = None
except Exception as e:
print(traceback.format_exc())
exit(1)
def getARGScmd():
parser = argparse.ArgumentParser(
description='worsica_resampling: Script to resample images from satellites sentinel 1/2 to 10m resolution')
parser.add_argument(
'-l',
'--list',
help='File with the name of the images to be resampled.',
required=False)
parser.add_argument(
'-b',
'--wktpolygon',
help='WKT polygon for bounding box for subset.',
metavar='N',
type=str,
nargs='+',
required=False)
args = parser.parse_args()
return args
def run_resample_rgb(procDicts):
try:
print('run_resample_rgb')
for procDict in procDicts:
if ('path' in procDict):
ACTUAL_PATH = procDict['path']
else:
ACTUAL_PATH = os.getcwd()
print('ACTUAL_PATH')
print(ACTUAL_PATH)
if not os.path.exists(ACTUAL_PATH + '/resampled'):
os.makedirs(ACTUAL_PATH + '/resampled', exist_ok=True)
if not os.path.exists(ACTUAL_PATH + '/auxResample'):
os.makedirs(ACTUAL_PATH + '/auxResample', exist_ok=True)
if not os.path.exists(ACTUAL_PATH + '/auxRGB'):
os.makedirs(ACTUAL_PATH + '/auxRGB', exist_ok=True)
worsicaResamplingRGB(procDicts)
return None
except Exception as e:
print(traceback.format_exc())
exit(1)
def run_resample(procDicts):
try:
print('run_resample')
for procDict in procDicts:
if ('path' in procDict):
ACTUAL_PATH = procDict['path']
else:
ACTUAL_PATH = os.getcwd()
print('ACTUAL_PATH')
print(ACTUAL_PATH)
if not os.path.exists(ACTUAL_PATH + '/resampled'):
os.makedirs(ACTUAL_PATH + '/resampled', exist_ok=True)
if not os.path.exists(ACTUAL_PATH + '/auxResample'):
os.makedirs(ACTUAL_PATH + '/auxResample', exist_ok=True)
if not os.path.exists(ACTUAL_PATH + '/auxRGB'):
os.makedirs(ACTUAL_PATH + '/auxRGB', exist_ok=True)
worsicaResampling(procDicts)
return None
except Exception as e:
print(traceback.format_exc())
exit(1)
def run_resample_waterleak_rgb(procDicts):
try:
print('run_resample_waterleak_rgb')
for procDict in procDicts:
if ('path' in procDict):
ACTUAL_PATH = procDict['path']
else:
ACTUAL_PATH = os.getcwd()
print('ACTUAL_PATH')
print(ACTUAL_PATH)
if not os.path.exists(ACTUAL_PATH + '/resampled'):
os.makedirs(ACTUAL_PATH + '/resampled', exist_ok=True)
if not os.path.exists(ACTUAL_PATH + '/auxResample'):
os.makedirs(ACTUAL_PATH + '/auxResample', exist_ok=True)
if not os.path.exists(ACTUAL_PATH + '/auxRGB'):
os.makedirs(ACTUAL_PATH + '/auxRGB', exist_ok=True)
worsicaResamplingWaterLeakRGB(procDicts)
return None
except Exception as e:
print(traceback.format_exc())
exit(1)
def run_resample_waterleak(procDicts):
try:
print('run_resample_waterleak')
for procDict in procDicts:
if ('path' in procDict):
ACTUAL_PATH = procDict['path']
else:
ACTUAL_PATH = os.getcwd()
print('ACTUAL_PATH')
print(ACTUAL_PATH)
if not os.path.exists(ACTUAL_PATH + '/resampled'):
os.makedirs(ACTUAL_PATH + '/resampled', exist_ok=True)
if not os.path.exists(ACTUAL_PATH + '/auxResample'):
os.makedirs(ACTUAL_PATH + '/auxResample', exist_ok=True)
if not os.path.exists(ACTUAL_PATH + '/auxRGB'):
os.makedirs(ACTUAL_PATH + '/auxRGB', exist_ok=True)
worsicaResamplingWaterLeak(procDicts)
return None
except Exception as e:
print(traceback.format_exc())
exit(1)
if __name__ == '__main__':
try:
args = getARGScmd()
projWinArgs = None
if args.list:
with open(args.list, "r") as fin:
imgs = fin.readlines()
imgs = [i.strip() for i in imgs]
else:
imgs = glob("*MSIL2A*.zip")
if args.wktpolygon:
# bbox = -9.28 38.68 -9.17 38.57